[gmx-users] more free energy questions
spoel at xray.bmc.uu.se
Tue Nov 11 22:37:01 CET 2003
On Tue, 2003-11-11 at 22:26, Ilya Chorny wrote:
> The balls are frozen so the configuration does not change. Only the
> water configuration could change. 50 kj/mol seems crazy because if each
> ball cost 50 kj/mol the total would be 250 not 99 as was obtained from
> the first simulation.
hm weird... You may have simple convergence problems though. I would
think that you need to do at least 10 steps to add a single ball.
There's is another problem though for which I don't know the solution:
if the balls are frozen that could also cost energy, i.e. if they could
move they might adopt another conformation. This is probably not taken
into account here.
> On Tue, 2003-11-11 at 13:16, David wrote:
> > On Tue, 2003-11-11 at 21:09, Ilya Chorny wrote:
> > > Hello,
> > >
> > > I ran a simulation to calculate the solvation free energy between soft
> > > spheres where the potential energy is (v=kt(3/r)^12 and six of the same
> > > spheres fused together at a distance of three angstroms. I ran the
> > > simulation at constant NVT. My box contains about 4000 H2O molecules and
> > > is 5 X 5 X 5 nm^3. The used ten windows used lambda values
> > > (0,.1,.2,.3,.4,.5,.6,.7,.8,.9,10) starting with one ball at lmabda = 0
> > > and ending up with 6 balls at lambda equals 1. I get a reasonable result
> > > of about 97 kj/mole. Previous work has shown the solvation free energy
> > > of one ball is about 20 kj/mol and I would expect six balls fused
> > > together to be less. I then take the six ball and mutate them to to five
> > > balls using just one lambda value of .5. Doing this I get crazy results
> > > (50-60 kj/mol). Any ideas what is going on? Any help would be greatly
> > > appreciated. Statistical convergence tests were used for all the
> > > simulations
> > Is it really tha crazy? It could be due to a particular conformation of
> > the balls.
> > >
> > > P.S. I noticed in my first simulation that the value I got at lambda =
> > > .5 was about the same as my overall result.
> > could be coincidence.
> > >
> > >
> > > Ilya
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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